|
| Status |
Public on Sep 02, 2016 |
| Title |
Wild-type, KLRG1-low [3c] |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
genotype: Wild-type
infection: Infected, KLRG1-low
|
| Treatment protocol |
P14 transgenic CD8+ T cells were isolated directly ex vivo from the spleen of naïve mice or those infected for eight days with LCMV-WE.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
3c
|
| Data processing |
FASTQ files were output using standard Illumina protocols and Illumina CASAVA sofware version 1.8.2.
Reads were aligned to the mouse genome with subread 1.4.4.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in RefSeq annotation.
Read counts from technical replicates of the same sample were summed.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE85302 |
KAT6A determines CD8+ T cell diversity via regulation of co-receptors |
|
| Relations |
| BioSample |
SAMN05521527 |
| SRA |
SRX2007436 |
